assemble sequences to

[hanshart]

Hi,
FASTQC can provide duplicate sequences during quality control of fastq data. But not all of them are really "unique" (=some of them are only partial sequences of a larger parental sequence (e.g. a contamination)). If I put all duplicate sequences in a text file (or FASTA), is it possible to "merge" those sequences by means of any software? thank you
(I allready tried Muscle but it seems to be not what i want)

[Torst]

Combining your sequences in this way will cause problems later on when de novo assembling or aligning, because it will change the coverage.

Why do you think it is 'contamination' ?

[hanshart]

Combining your sequences in this way will cause problems later on when de novo assembling or aligning, because it will change the coverage.

Why do you think it is 'contamination' ?

Its rRNA. But many sequences occur more than once. Sequences that occur many times could be identified this way and filtered out in the next experiments. That's the idea behind the question.

[Torst]

So this is RNA-Seq data, not genomic DNA. If you know what species it is, align all the reads to the 8/16/23s rRNA sequence, and then pass the UNALIGNED reads to FastQC.